Trichomonas vaginalis is an anaerobic, flagellated haploid protozoan. Trichomonas vaginalis is sexually transmitted in humans, causing >7 million infections annually in the United States. Infection with Trichomonas vaginalis (i.e., trichomoniasis) is a common cause of vaginitis, and is associated with HIV transmission and obstetric complications. Patients suffering from Trichomonas vaginalis are normally treated with antibiotics such as metronidazole. Metronidazole is a pro-drug believed to undergo reduction to a nitro radical anion form by anaerobic metabolism. The anion form of metronidazole is thought to kill the microorganisms by non-specifically damaging proteins and DNA in Trichomonas vaginalis. 
Despite that metronidazole treatment is reported to be 85-95% effective, there is an estimated 2.5%-10% clinical isolates of Trichomonas vaginalis that exhibit varying degrees of metronidazole resistance. Given the significant occurrence of trichomoniasis, emerging metronidazole resistance in Trichomonas vaginalis is posing a significant problem to public health.
It is suggested that metronidazole resistance in vitro may result in loss of hydrogenosome enzymes such as hydrogenase, ferredoxin and pyruvate:ferredoxin oxidoreductase. These enzymes are thought to play a role in reducing metronidazole to its active form. The cytoplasmic enzyme thioredoxin reductase may similarly contribute in metronidazole resistance.
Current methodology for detecting metronidazole resistance in Trichomonas vaginalis requires culturing the microorganism in a laboratory under serial dilutions of antibiotic (e.g., metronidazole) to determine the minimum lethal concentration. This culturing methodology suffers many problems: (a) it requires a viable Trichomonas vaginalis culture derived from a patient; (b) it requires highly trained personnel; and (c) it is time-consuming and often requires weeks to obtain results.
Accordingly, there is a continuing need for an improved method that allows rapid and reliable detection of metronidazole resistance in Trichomonas vaginalis without culturing. The present inventors resolved all the prior art deficiency and discovered specific SNPs that are useful in detecting metronidazole resistance in Trichomonas vaginalis. 